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Indigenous grains for food production have the potential to combat food insecurity and poverty in Africa. The aim of the study was to determine the effect of sourdough fermentation on the acidity, microbiological quality, microbial diversity and rheological properties of three underutilized African cereals. The sourdoughs had pH ranging from 3.9 to 4.1. Finger millet and pearl millet sourdoughs had LAB counts >7 log cfu g−1 indicating they are suitable for use as starter culture(s). Microbial diversity was determined using culture dependent techniques and the identity of isolates was established using 16S rRNA gene sequencing. This showed the presence of Bacillus , Brevibacillus , Acinetobacter and Pediococcus species in the sourdoughs. An occurrence of Candida glabrata was observed in finger millet sourdough. Sourdough fermentation resulted in significant increases (p < 0.05) in the peak, trough and final viscosity of pearl millet and sorghum. A lower setback in the three samples indicated improved shelf-life. Starter culture(s) were identified that might be used in the production of gluten-free baked foods as a result of sourdough fermentation. [ABSTRACT FROM AUTHOR]